Stream: IG creation
Topic: Missing 'fragment-summary-table.html' file
Rob Hausam (Sep 02 2021 at 18:29):
I've recently (in the past 24 -48 hours) started getting this Jekyll failure:
Jekyll: Source: /Users/rhausam/git-repo/fhir-ips-2/temp/pages (02:59.0834)
Jekyll: Generating... (02:59.0834)
Jekyll has failed. Complete output from running Jekyll: Liquid Exception: Could not locate the included file 'fragment-summary-table.html' in any of ["/Users/rhausam/git-repo/fhir-ips-2/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside yo (03:00.0464)
Note: Check that Jekyll is installed correctly (03:00.0464)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (03:00.0465)
(03:00.0465)
Use -? to get command line help (03:00.0466)
(03:00.0466)
Stack Dump (for debugging): (03:00.0466)
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:153)
at org.hl7.fhir.igtools.publisher.Publisher.runJekyll(Publisher.java:5801)
at org.hl7.fhir.igtools.publisher.Publisher.runTool(Publisher.java:5723)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:5114)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:908)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:752)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8664)
At first it was only occurring in the CI build - so I missed seeing it initially. But after deleting my local package cache I'm now getting the same error on my local build.
@Grahame Grieve @Mark Iantorno @Jose Costa Teixeira @Lloyd McKenzie
Jose Costa Teixeira (Sep 02 2021 at 18:30):
- did you get today's ig publisher?
Jose Costa Teixeira (Sep 02 2021 at 18:30):
- do you have a repo for me to look into it?
Rob Hausam (Sep 02 2021 at 18:33):
Yes, I've updated to 1.1.79 and that didn't change anything.
https://github.com/HL7/fhir-ips/tree/connectathon-2
Jose Costa Teixeira (Sep 02 2021 at 18:58):
first I am finding this issue with the spreadsheet names - is this known yet?
Exception generating resource C:\fhir-ips-connectathon-2\input\vocabulary\valueset-medication-example-uv-ips::ValueSet/medication-example-uv-ips: The workbook already contains a sheet named 'Include from National drug codes' (02:57.0919)
java.lang.IllegalArgumentException: The workbook already contains a sheet named 'Include from National drug codes'
at org.apache.poi.xssf.usermodel.XSSFWorkbook.validateSheetName(XSSFWorkbook.java:910)
at org.apache.poi.xssf.usermodel.XSSFWorkbook.createSheet(XSSFWorkbook.java:863)
at org.hl7.fhir.r5.renderers.spreadsheets.ValueSetSpreadsheetGenerator.genIncludeSystem(ValueSetSpreadsheetGenerator.java:117)
at org.hl7.fhir.r5.renderers.spreadsheets.ValueSetSpreadsheetGenerator.genInclude(ValueSetSpreadsheetGenerator.java:87)
at org.hl7.fhir.r5.renderers.spreadsheets.ValueSetSpreadsheetGenerator.renderValueSet(ValueSetSpreadsheetGenerator.java:40)
at org.hl7.fhir.igtools.publisher.Publisher.generateOutputsValueSet(Publisher.java:7815)
Rob Hausam (Sep 02 2021 at 19:00):
Yes, there are a bunch of these errors since Grahame added the terminology spreadsheets to the publisher. But they didn't stop my local builds, until I deleted the package cache in .fhir. I've been ignoring those errors for the moment.
Jose Costa Teixeira (Sep 02 2021 at 19:03):
i'm currently stuck. Jekyll hangs
Rob Hausam (Sep 02 2021 at 19:04):
Yes - that's exactly the issue.
Jose Costa Teixeira (Sep 02 2021 at 19:04):
(or the thing that comes after Jenkins
Jekyll: Generating... (03:22.0242)
Sending usage stats failed: Connection timed out: connect
Rob Hausam (Sep 02 2021 at 19:04):
Oh - different issue. :smile:
Rob Hausam (Sep 02 2021 at 19:07):
On a different IPS branch, I have another issue. On the 'connectathon' branch (which uses FSH and has more complicated value sets but less slicing), I now get this issue:
onLoad:
Root directory: /Users/rhausam/git-repo/fhir-ips (00:12.0967)
Core Package hl7.fhir.r4.core#4.0.1
Terminology Cache is at /Users/rhausam/git-repo/fhir-ips/input-cache/txcache. 15 files in cache (00:16.0960)
Connect to Terminology Server at http://tx.fhir.org (00:32.0348)
Load Package hl7.fhir.pubpack#0.0.9
Load Package hl7.fhir.xver-extensions#0.0.5
Load Package hl7.terminology.r4#2.1.0
Initialization complete (00:34.0314)
Fetch http://hl7.org/fhir/uv/ips/package-list.json for version check (00:34.0316)
Load Content (00:34.0459)
Translating CQL source (00:34.0521)
Translating CQL source in folder /Users/rhausam/git-repo/fhir-ips/input/cql (00:34.0521)
Publishing Content Failed: No Source directories to scan found (00:34.0525)
(00:34.0526)
Use -? to get command line help (00:34.0526)
(00:34.0526)
Stack Dump (for debugging): (00:34.0526)
org.hl7.fhir.exceptions.FHIRException: No Source directories to scan found
at org.hl7.fhir.igtools.publisher.SimpleFetcher.scan(SimpleFetcher.java:301)
at org.hl7.fhir.igtools.publisher.Publisher.loadResources(Publisher.java:3705)
at org.hl7.fhir.igtools.publisher.Publisher.load(Publisher.java:3200)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:892)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:752)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8664)
That issue also first appeared in the CI build. It was not occurring for me locally until I deleted the package cache.
Jose Costa Teixeira (Sep 02 2021 at 19:25):
still stuck. I'm giving up
Rob Hausam (Sep 02 2021 at 19:28):
Thanks for trying to look at it. This is a big showstopper for me now.
@Grahame Grieve
Bryn Rhodes (Sep 05 2021 at 22:37):
I’m getting this error in qi-core now as well, but it builds locally without any issues. Not sure what to try next?
Bryn Rhodes (Sep 05 2021 at 22:38):
Missing ‘fragment-summary-table.html’
Rob Hausam (Sep 05 2021 at 23:17):
@Bryn Rhodes I fixed this issue for my builds by using the #current template (in ig.ini). Eventually I (we) should be able to move it back, but that was still failing when I last tried it (I think a little over 24 hours ago).
Grahame Grieve (Sep 06 2021 at 00:28):
or you can clean out your package cache
Grahame Grieve (Sep 06 2021 at 00:28):
this won't be an issue after the next release
Rob Hausam (Sep 06 2021 at 00:42):
I just tried removing #current from the template again and deleting the package cache, and when I re-run the build I get the same Liquid Exception: Could not locate the included file 'fragment-summary-table.html' in any of ... message that I've been getting before - #current still seems to be needed for now.
@Grahame Grieve
Grahame Grieve (Sep 06 2021 at 00:43):
the released package is the same as current at this time
Rob Hausam (Sep 06 2021 at 00:44):
So it shouldn't be different - but it is.
Bryn Rhodes (Sep 06 2021 at 01:42):
That did the trick for QI-Core as well, thank you @Rob Hausam
Last updated: Apr 12 2022 at 19:14 UTC
